Note that the brake pedal rod MUST enter the master cylinder dead on straight in a manual brake scenario. Discussions of drilling different holes in the brake pedal in efforts to alter brake pedal ratios are not valid because the brake pedal rod will then enter the backside of the MC at an inappropriate angle causing linkage bind, MC failure from extreme side loading of the pistons, and even possible complete failure of the brake pedal rod linkage entirely.
Summary? You MUST keep your brake rod connection in the factory manual brake top hole - no if's, and's, or but's about it.